From: "Charles C. Berry" <ccberry@ucsd.edu>
To: "Cook, Malcolm" <MEC@stowers.org>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround
Date: Thu, 1 Oct 2015 14:56:57 -0700 [thread overview]
Message-ID: <alpine.OSX.2.20.1510011443090.1095@charles-berrys-macbook.local> (raw)
In-Reply-To: <e23d5e509a6740f19e355d07757c30d7@exchsrv2.sgc.loc>
On Thu, 1 Oct 2015, Cook, Malcolm wrote:
> Hello ,
>
> I am not sure what the best solution is, but, in my hands using Org-mode
> version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra
> prompts left in output" is over-aggressive and will trim session :output
> at lines consisting exclusively of blanks and periods such as produced
> when printing a BioConductor 'Views' object which wants to appear as
I'd try (for example):
#+BEGIN_SRC R :results value raw drawer :session
require(GenomicRanges)
capture.output(show(GRanges(seqnames=rep("a",100),
IRanges(start=1:100,width=1),strand=rep("*",100))))
#+END_SRC
rather than messing with the regexp.
>
>
> I offer as a possible workaround the following:
>
> So far, I have had good success having removed provision for allowing leading whitespace by changing the regexp org-babel-R-evaluate-session from
> "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)"
> to
> "^\\([>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)"
>
> But I don't know all the test cases so, YMMV....
Just guessing that the things that `(setq ess-eval-visibly nil)' generates
(e.g., + + + + + > ) won't behave using your version.
HTH,
Chuck
next prev parent reply other threads:[~2015-10-01 21:57 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-10-01 19:59 BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround Cook, Malcolm
2015-10-01 21:56 ` Charles C. Berry [this message]
2015-10-01 23:15 ` Cook, Malcolm
2015-10-08 19:24 ` Charles C. Berry
2015-10-08 20:41 ` Cook, Malcolm
2015-11-05 12:57 ` Nicolas Goaziou
2015-11-06 23:11 ` Charles C. Berry
2015-11-07 21:30 ` Charles C. Berry
2015-11-07 21:41 ` Nicolas Goaziou
2015-11-07 23:22 ` Cook, Malcolm
2015-11-08 0:32 ` Charles C. Berry
2015-11-09 20:04 ` Cook, Malcolm
2015-11-09 20:56 ` Charles C. Berry
2015-11-09 22:11 ` Cook, Malcolm
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